BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013226.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 3,499,868 number of mapped reads = 3,133,867 (89.54%) number of supplementary alignments = 18,299 (0.52%) number of secondary alignments = 0 number of mapped bases = 206,075,939 bp number of sequenced bases = 205,989,596 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 151,717 duplication rate = 3.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1413 >>>>>>> ACTG content number of A's = 56,614,377 bp (27.48%) number of C's = 37,339,869 bp (18.13%) number of T's = 65,680,273 bp (31.89%) number of G's = 46,352,283 bp (22.5%) number of N's = 2,794 bp (0%) GC percentage = 40.63% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 1,492,860 number of insertions = 14,468 mapped reads with insertion percentage = 0.46% number of deletions = 50,250 mapped reads with deletion percentage = 1.59% homopolymer indels = 46.06% >>>>>>> Coverage mean coverageData = 0.0666X std coverageData = 0.6228X There is a 5.4% of reference with a coverageData >= 1X There is a 0.88% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 12962033 0.05200401486662695 0.7105224461079465 chr2 243199373 23046303 0.09476300335692066 0.7525495689068676 chr3 198022430 12942637 0.06535944943206687 0.2989229056073602 chr4 191154276 15824113 0.08278189392948762 0.35480665267977113 chr5 180915260 12360510 0.06832209731782714 0.31279462996906454 chr6 171115067 10260572 0.059962995543811466 0.5319074803342692 chr7 159138663 18659302 0.11725184595776075 1.7575987748653383 chr8 146364022 9810406 0.0670274420308018 0.6950921274213454 chr9 141213431 6858004 0.04856481392340081 0.47822690673207197 chr10 135534747 7711282 0.05689524030321169 0.4584613707815744 chr11 135006516 8571694 0.06349096513237924 0.40958211133097455 chr12 133851895 5209649 0.038920995477875 0.24877518547745667 chr13 115169878 6769251 0.05877622793001482 0.2860302831988543 chr14 107349540 4598157 0.04283350445656311 0.2856865447922842 chr15 102531392 5224585 0.05095595503082607 0.27487525420833364 chr16 90354753 7094312 0.07851620157713231 0.3692342419045296 chr17 81195210 5945955 0.07323036666818153 0.4058073515188301 chr18 78077248 6268173 0.08028168462085139 0.8344164018714331 chr19 59128983 3741029 0.06326895559830617 0.6473001880505225 chr20 63025520 3543978 0.056230841094210726 0.29755038546382984 chr21 48129895 4400316 0.09142583834849421 0.3990463879403693 chr22 51304566 1568306 0.03056854627714812 0.2019067631641803 chrMT 16571 30979 1.8694707621748838 1.8346015258536117 chrX 155270560 12217881 0.07868768554708633 0.41153520417649203 chrY 59373566 456512 0.0076888088547688044 0.15507881518006528